Statement of Work.pdf

Statement of Work (SOW)

Project: Chromatin mapping of alfalfa

GENERAL INFORMATION

1.0 Scope of Work:

The service provider will perform chromatin mapping of alfalfa DNA, often called Hi-C mapping or Proximity Ligation mapping from plant samples provided by Plant Science Research Unit located at the University of Minnesota, St. Paul, MN. The goal of the ARS project is to scaffold the draft assembly of the alfalfa genome into haplotypes. Due to the tetraploid nature of alfalfa, each of the four sets of chromosomes has a different DNA sequence, requiring chromatin mapping to assemble the DNA sequence scaffolds and identify the four haplotypes.

2.0 Background:

Developing genomic resources for alfalfa has lagged behind other crop species.

There is currently no reference genome for alfalfa cultivars grown in the US. The lack of a reference genome sequence for tetraploid alfalfa impedes progress in molecular breeding methods to improve alfalfa including genomic selection, transgenic approaches to crop improvement, and genome editing. The goal of this project is to correctly assemble the DNA sequences previously obtained into the correct order and identify the four haplotypes. The lab requires chromatin mapping (Hi-C mapping) of alfalfa.

CONTRACTOR REQUIREMENTS

2.0 Technical Requirements/Tasks:

A plant sample will be shipped to the service provider on dry ice.

The service provider will perform these specific tasks:

1. Construct a proximity ligation library from the plant sample.

2. Sequence approximately 2 million paired end 75 bp reads and map the data back to the draft genome assembly to assess library quality.

3. Sequence the proximity ligation library to a target depth of 30X.

4. Scaffold the draft assembly through software pipelines using the proximity ligation data.

5. The provider may perform a TAD analysis of the genome generated from the proximity ligation library if warranted by the complexity of the genome and the output of the scaffolding pipeline.

Delivery schedule: Twenty weeks from the time of sample submission.

3.0 Government Furnished:

The service provider is solely responsible for the entire service. There will be no support or use of federal facility by the service provider. The service provider will submit a report to end user at the end of the completion of the service.

4.0 Deliverables / Schedule:

Deliverables will consist of:

• The scaffold assembly in FASTA format

• A report summarizing key assembly statistics, features of the proximity ligation library, and a linkage density plot of the proximity ligation library data

• A table detailing the breaks made to the input scaffolds

• A table describing the position of the input assembly scaffolds within the final scaffolds

• BAM file(s) containing alignments of the proximity ligation library read pairs mapped to the draft assembly TAD Analysis deliverables, if applicable, include:

• TAD calls at 10kbp, 25kbp, and 50kbp

• CTCF binding sites

• A/B compartmental organization

• Isochore locations

• Guide to loading and viewing data in HiGlass

• Summary report

• QC report

• Raw ILMN data from deep sequencing the PL library

All data generated by the vendor will be submitted to the ARS within 90 calendar days from date of receipt.